The three-dimensional structure of shikimate kinase

Area of Science:

• Biochemistry
• Structural Biology
• Enzymology

Background:

• Shikimate kinase (EcSK) is crucial in the shikimate pathway, essential for synthesizing aromatic amino acids in bacteria.
• Understanding the three-dimensional structure of EcSK provides insights into its catalytic mechanism and potential drug targets.

Purpose of the Study:

• To determine the high-resolution three-dimensional structure of shikimate kinase from Erwinia chrysanthemi.
• To elucidate the enzyme's conformational changes upon ligand binding and compare its structure to related enzymes.

Main Methods:

• X-ray crystallography using multiple isomorphous replacement.
• Determination of two models: a 1.9 Å high-resolution model and a 2.6 Å model with bound Mg-ADP.
• Difference Fourier calculations to identify ligand-binding sites.

Main Results:

• The structure reveals an α/β protein with topology similar to adenylate kinase, featuring a P-loop core and flexible domains.
• Major conformational changes and induced fit movements were observed upon ligand binding.
• Identified a distinct Mg2+ binding mode and characterized the adenine-binding motif (I/VDAXQ/NXP).
• The shikimate binding site was mapped to the location of the AMP-binding site in adenylate kinase.

Conclusions:

• Shikimate kinase exhibits significant structural plasticity, undergoing induced fit upon substrate binding.
• Structural comparisons with adenylate kinase highlight conserved and divergent features in enzyme active sites.
• The determined structure provides a foundation for understanding shikimate kinase function and designing inhibitors.